"The misconduct exhibits great variety. It is widespread. It is deep-seated."
He believes what has been uncovered is just the "small tip of an enormous iceberg".
"It is clear that in many parts of the world constituted by Australian trade union officials, there is room for louts, thugs, bullies, thieves, perjurers, those who threaten violence, errant fiduciaries and organisers of boycotts," he said.
He highlighted six unions and a slew of officials from various unions have been referred to prosecutors over possible criminal conduct, including Mr Melham, the former Victorian state secretary of the Australian Workers Union (AWU).
"Cesar Melhem has been responsible for numerous actions favouring the interests of the union over the members which may be breaches of legal duty," Mr Heydon said.
He referred Mr Melham to Victorian prosecutors for consideration of possible corruption and false accounting charges.
Former Health Services Union secretary Kathy Jackson has also been referred to prosecutors to consider whether she should be charged for obtaining property and financial advantage by deception, the report says.
Mr Heydon has also asked the Victorian Commissioner of Police to investigate whether she may have given false or misleading evidence.
The NSW branch of the Construction, Forestry, Mining and Energy Union has been referred to the corporate watchdog and Mr Heydon has asked the NSW government to consider an inquiry into it "concerning charitable fundraising".
The AWU has also been referred to Victorian prosecutors over deals with Cleanevent, Thiess John Holland, Chiquita Mushrooms, ACI Operations and Winslow Constructors.
John Holland Pty Ltd and Chiquita Mushrooms have also been referred to prosecutors.
Liberal Senator Eric Abetz says the report vindicates the commission and denounced Labor leader Bill Shorten who said it was a political witchhunt set up by former prime minister Tony Abbott.
"I think the Labor Party, especially Mr Shorten, should now say 'It's time to raise the white flag, we do need as a nation to get rid of this corruption'," Senator Abetz said in Hobart.
"For Bill Shorten to continue to run the activities that he has of allowing his frontbenchers to denigrate the Royal Commissioner badly backfired, badly misjudged and it shows why Bill Shorten should never become the Prime Minister of our country."
The report has made 79 recommendations for sweeping reform of the workplace system, including that all regulatory functions of the Fair Work Commission relating to registered organisations be transferred to a new independent regulator.
The Registered Organisations Commission would have strengthened enforcement powers and investigative powers similar to those of the Australian Securities and Investments Commission.
Mr Heydon was also damning of many of the 505 witnesses in the 21-month long royal commission.
"There has been much perjury. A huge amount of the testimony given in hearings has been false to the knowledge of the witnesses," he said.
-AAP